Preliminary data exploration
Contaminant ASVs were identified with the prevalence method using the decontam package.
Plant measures overview
Scaled-centered plant ‘health’ measures, broken down by treatment factors.
Figure 1
Model output
Formula: value ~ drought * host * site + (1|block))
| effect | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|
| fixed | (Intercept) | 0.152 | 0.270 | 0.563 | 19.346 | 0.580 |
| fixed | droughtND | -0.119 | 0.266 | -0.449 | 458.953 | 0.654 |
| fixed | hostCeanothus velutinus | -0.619 | 0.266 | -2.329 | 458.953 | 0.020 |
| fixed | inoculum_site2 | 0.274 | 0.266 | 1.029 | 458.953 | 0.304 |
| fixed | inoculum_site3 | -0.677 | 0.266 | -2.547 | 458.953 | 0.011 |
| fixed | inoculum_site4 | 0.370 | 0.266 | 1.394 | 458.953 | 0.164 |
| fixed | inoculum_site5 | 0.485 | 0.266 | 1.826 | 458.953 | 0.069 |
| fixed | inoculum_site6 | 0.259 | 0.266 | 0.974 | 458.953 | 0.331 |
| fixed | inoculum_siteSterile | -0.435 | 0.266 | -1.636 | 458.953 | 0.103 |
| fixed | droughtND:hostCeanothus velutinus | 0.758 | 0.382 | 1.986 | 458.980 | 0.048 |
| fixed | droughtND:inoculum_site2 | -0.171 | 0.376 | -0.455 | 458.953 | 0.650 |
| fixed | droughtND:inoculum_site3 | -0.124 | 0.381 | -0.325 | 464.972 | 0.745 |
| fixed | droughtND:inoculum_site4 | 0.861 | 0.376 | 2.290 | 458.953 | 0.022 |
| fixed | droughtND:inoculum_site5 | -0.209 | 0.376 | -0.556 | 458.953 | 0.578 |
| fixed | droughtND:inoculum_site6 | 0.004 | 0.376 | 0.010 | 458.953 | 0.992 |
| fixed | droughtND:inoculum_siteSterile | 0.374 | 0.376 | 0.994 | 458.953 | 0.321 |
| fixed | hostCeanothus velutinus:inoculum_site2 | -0.070 | 0.376 | -0.187 | 458.953 | 0.852 |
| fixed | hostCeanothus velutinus:inoculum_site3 | 0.469 | 0.376 | 1.247 | 458.953 | 0.213 |
| fixed | hostCeanothus velutinus:inoculum_site4 | 0.063 | 0.386 | 0.164 | 459.021 | 0.870 |
| fixed | hostCeanothus velutinus:inoculum_site5 | -0.005 | 0.376 | -0.013 | 458.953 | 0.990 |
| fixed | hostCeanothus velutinus:inoculum_site6 | 0.004 | 0.386 | 0.010 | 459.009 | 0.992 |
| fixed | hostCeanothus velutinus:inoculum_siteSterile | 0.603 | 0.386 | 1.564 | 459.021 | 0.118 |
| fixed | droughtND:hostCeanothus velutinus:inoculum_site2 | 0.243 | 0.536 | 0.453 | 458.967 | 0.651 |
| fixed | droughtND:hostCeanothus velutinus:inoculum_site3 | -0.364 | 0.540 | -0.675 | 463.713 | 0.500 |
| fixed | droughtND:hostCeanothus velutinus:inoculum_site4 | -1.004 | 0.543 | -1.849 | 459.043 | 0.065 |
| fixed | droughtND:hostCeanothus velutinus:inoculum_site5 | 0.176 | 0.536 | 0.328 | 458.967 | 0.743 |
| fixed | droughtND:hostCeanothus velutinus:inoculum_site6 | -0.412 | 0.543 | -0.760 | 458.986 | 0.448 |
| fixed | droughtND:hostCeanothus velutinus:inoculum_siteSterile | -0.592 | 0.543 | -1.090 | 459.043 | 0.276 |
Inoculum communities overview
Taxonomic overview
Bacteria
Figure 2
Alpha diversity
Effect of Shannon diversity on plant measures
## overall_transformed_plant_value ~ Shannon * host * drought *
## inoculum_site + (1 | block)
## <environment: 0x556928702540>
Table 2
| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | -1.226 | 0.507 | -2.417 | 122.238 | 0.017 |
| fixed | NA | Shannon | 0.301 | 0.101 | 2.993 | 609.763 | 0.003 |
| fixed | NA | hostCeanothus velutinus | 0.984 | 2.559 | 0.385 | 610.106 | 0.701 |
| fixed | NA | droughtND | -0.187 | 2.351 | -0.079 | 609.423 | 0.937 |
| fixed | NA | inoculum_site2 | 1.378 | 1.915 | 0.720 | 609.868 | 0.472 |
| fixed | NA | inoculum_site3 | 1.749 | 4.502 | 0.389 | 610.099 | 0.698 |
| fixed | NA | inoculum_site4 | 1.827 | 1.868 | 0.978 | 610.007 | 0.328 |
| fixed | NA | inoculum_site5 | 6.697 | 3.448 | 1.942 | 609.951 | 0.053 |
| fixed | NA | inoculum_site6 | 6.414 | 1.849 | 3.470 | 610.406 | 0.001 |
| fixed | NA | inoculum_siteSterile | 7.260 | 2.633 | 2.757 | 609.891 | 0.006 |
| fixed | NA | Shannon:hostCeanothus velutinus | -0.301 | 0.424 | -0.709 | 610.132 | 0.478 |
| fixed | NA | Shannon:droughtND | -0.033 | 0.409 | -0.080 | 609.263 | 0.936 |
| fixed | NA | hostCeanothus velutinus:droughtND | 17.677 | 8.477 | 2.085 | 611.147 | 0.037 |
| fixed | NA | Shannon:inoculum_site2 | -0.223 | 0.345 | -0.647 | 609.967 | 0.518 |
| fixed | NA | Shannon:inoculum_site3 | -0.477 | 0.754 | -0.633 | 610.113 | 0.527 |
| fixed | NA | Shannon:inoculum_site4 | -0.334 | 0.352 | -0.948 | 610.051 | 0.344 |
| fixed | NA | Shannon:inoculum_site5 | -1.150 | 0.612 | -1.879 | 609.963 | 0.061 |
| fixed | NA | Shannon:inoculum_site6 | -1.153 | 0.330 | -3.495 | 610.521 | 0.001 |
| fixed | NA | Shannon:inoculum_siteSterile | -1.391 | 0.457 | -3.045 | 609.950 | 0.002 |
| fixed | NA | hostCeanothus velutinus:inoculum_site2 | -1.457 | 3.239 | -0.450 | 610.782 | 0.653 |
| fixed | NA | hostCeanothus velutinus:inoculum_site3 | -2.040 | 6.432 | -0.317 | 611.675 | 0.751 |
| fixed | NA | hostCeanothus velutinus:inoculum_site4 | -5.726 | 4.534 | -1.263 | 610.573 | 0.207 |
| fixed | NA | hostCeanothus velutinus:inoculum_site5 | -9.239 | 6.982 | -1.323 | 610.067 | 0.186 |
| fixed | NA | hostCeanothus velutinus:inoculum_site6 | -16.444 | 7.791 | -2.111 | 608.880 | 0.035 |
| fixed | NA | hostCeanothus velutinus:inoculum_siteSterile | -7.195 | 4.427 | -1.625 | 611.688 | 0.105 |
| fixed | NA | droughtND:inoculum_site2 | -1.482 | 3.252 | -0.456 | 608.582 | 0.649 |
| fixed | NA | droughtND:inoculum_site3 | 1.646 | 5.810 | 0.283 | 615.792 | 0.777 |
| fixed | NA | droughtND:inoculum_site4 | 2.497 | 3.822 | 0.653 | 609.716 | 0.514 |
| fixed | NA | droughtND:inoculum_site5 | -2.968 | 4.505 | -0.659 | 609.380 | 0.510 |
| fixed | NA | droughtND:inoculum_site6 | -3.067 | 3.816 | -0.804 | 609.535 | 0.422 |
| fixed | NA | droughtND:inoculum_siteSterile | -5.102 | 4.529 | -1.127 | 608.940 | 0.260 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND | -2.903 | 1.447 | -2.007 | 611.120 | 0.045 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site2 | 0.265 | 0.551 | 0.481 | 610.838 | 0.631 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site3 | 0.467 | 1.042 | 0.448 | 611.699 | 0.654 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site4 | 1.033 | 0.764 | 1.352 | 610.587 | 0.177 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site5 | 1.626 | 1.148 | 1.416 | 610.110 | 0.157 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site6 | 2.803 | 1.253 | 2.237 | 608.849 | 0.026 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_siteSterile | 1.380 | 0.739 | 1.868 | 611.677 | 0.062 |
| fixed | NA | Shannon:droughtND:inoculum_site2 | 0.315 | 0.576 | 0.546 | 608.588 | 0.585 |
| fixed | NA | Shannon:droughtND:inoculum_site3 | -0.280 | 0.990 | -0.283 | 615.999 | 0.777 |
| fixed | NA | Shannon:droughtND:inoculum_site4 | -0.250 | 0.673 | -0.372 | 609.580 | 0.710 |
| fixed | NA | Shannon:droughtND:inoculum_site5 | 0.562 | 0.795 | 0.706 | 609.339 | 0.480 |
| fixed | NA | Shannon:droughtND:inoculum_site6 | 0.615 | 0.686 | 0.897 | 609.495 | 0.370 |
| fixed | NA | Shannon:droughtND:inoculum_siteSterile | 1.016 | 0.779 | 1.304 | 608.901 | 0.193 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site2 | -13.825 | 9.008 | -1.535 | 610.965 | 0.125 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site3 | -23.837 | 11.167 | -2.135 | 614.160 | 0.033 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site4 | -12.860 | 9.807 | -1.311 | 610.900 | 0.190 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site5 | -6.875 | 11.623 | -0.591 | 609.219 | 0.554 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site6 | 1.508 | 11.603 | 0.130 | 609.041 | 0.897 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_siteSterile | -11.042 | 9.889 | -1.117 | 610.051 | 0.265 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 | 2.325 | 1.546 | 1.503 | 610.908 | 0.133 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 | 4.032 | 1.880 | 2.145 | 614.514 | 0.032 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 | 2.020 | 1.678 | 1.204 | 610.839 | 0.229 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 | 1.194 | 1.944 | 0.614 | 609.262 | 0.539 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 | -0.260 | 1.938 | -0.134 | 609.046 | 0.893 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile | 1.757 | 1.684 | 1.044 | 609.997 | 0.297 |
| ran_pars | block | sd__(Intercept) | 0.537 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.812 | NA | NA | NA | NA |
Fungi
Figure 3
Alpha diversity
Effect of Shannon diversity on plant measures
Table 3
## overall_transformed_plant_value ~ Shannon * host * drought *
## inoculum_site + (1 | block)
## <environment: 0x556928702540>
| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | 0.849 | 0.357 | 2.379 | 175.175 | 0.018 |
| fixed | NA | Shannon | -0.494 | 0.187 | -2.639 | 781.982 | 0.008 |
| fixed | NA | hostCeanothus velutinus | -0.898 | 0.731 | -1.228 | 781.153 | 0.220 |
| fixed | NA | droughtND | -0.100 | 0.586 | -0.170 | 780.300 | 0.865 |
| fixed | NA | inoculum_site2 | -0.307 | 0.780 | -0.394 | 780.746 | 0.694 |
| fixed | NA | inoculum_site3 | -0.923 | 0.625 | -1.478 | 782.135 | 0.140 |
| fixed | NA | inoculum_site4 | -0.526 | 0.439 | -1.199 | 778.320 | 0.231 |
| fixed | NA | inoculum_site5 | -0.416 | 0.899 | -0.463 | 779.825 | 0.644 |
| fixed | NA | inoculum_site6 | 1.264 | 0.950 | 1.330 | 781.558 | 0.184 |
| fixed | NA | inoculum_siteSterile | -0.601 | 0.835 | -0.720 | 779.664 | 0.472 |
| fixed | NA | Shannon:hostCeanothus velutinus | 0.253 | 0.368 | 0.686 | 781.374 | 0.493 |
| fixed | NA | Shannon:droughtND | 0.071 | 0.391 | 0.182 | 780.743 | 0.856 |
| fixed | NA | hostCeanothus velutinus:droughtND | 0.423 | 1.009 | 0.419 | 779.046 | 0.676 |
| fixed | NA | Shannon:inoculum_site2 | 0.464 | 0.412 | 1.127 | 780.882 | 0.260 |
| fixed | NA | Shannon:inoculum_site3 | 0.286 | 0.407 | 0.703 | 782.551 | 0.482 |
| fixed | NA | Shannon:inoculum_site4 | 0.472 | 0.272 | 1.733 | 778.563 | 0.084 |
| fixed | NA | Shannon:inoculum_site5 | 0.561 | 0.521 | 1.077 | 779.847 | 0.282 |
| fixed | NA | Shannon:inoculum_site6 | -0.426 | 0.463 | -0.921 | 781.844 | 0.357 |
| fixed | NA | Shannon:inoculum_siteSterile | 0.148 | 0.573 | 0.259 | 779.993 | 0.796 |
| fixed | NA | hostCeanothus velutinus:inoculum_site2 | -1.597 | 1.728 | -0.924 | 783.189 | 0.356 |
| fixed | NA | hostCeanothus velutinus:inoculum_site3 | 1.317 | 1.087 | 1.212 | 779.267 | 0.226 |
| fixed | NA | hostCeanothus velutinus:inoculum_site4 | 1.081 | 1.230 | 0.879 | 780.948 | 0.379 |
| fixed | NA | hostCeanothus velutinus:inoculum_site5 | 0.875 | 1.388 | 0.630 | 778.872 | 0.529 |
| fixed | NA | hostCeanothus velutinus:inoculum_site6 | -1.300 | 1.398 | -0.930 | 779.092 | 0.353 |
| fixed | NA | hostCeanothus velutinus:inoculum_siteSterile | 3.604 | 2.018 | 1.786 | 782.650 | 0.074 |
| fixed | NA | droughtND:inoculum_site2 | -0.134 | 1.054 | -0.128 | 778.928 | 0.899 |
| fixed | NA | droughtND:inoculum_site3 | -0.704 | 0.936 | -0.752 | 783.662 | 0.452 |
| fixed | NA | droughtND:inoculum_site4 | 0.278 | 0.730 | 0.381 | 779.650 | 0.703 |
| fixed | NA | droughtND:inoculum_site5 | 1.726 | 1.308 | 1.320 | 779.211 | 0.187 |
| fixed | NA | droughtND:inoculum_site6 | -1.982 | 1.176 | -1.686 | 781.343 | 0.092 |
| fixed | NA | droughtND:inoculum_siteSterile | -0.932 | 1.574 | -0.592 | 779.049 | 0.554 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND | 0.107 | 0.564 | 0.189 | 779.603 | 0.850 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site2 | 0.401 | 0.759 | 0.529 | 783.178 | 0.597 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site3 | -0.635 | 0.624 | -1.017 | 779.000 | 0.309 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site4 | -0.621 | 0.606 | -1.025 | 781.143 | 0.306 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site5 | -0.621 | 0.703 | -0.883 | 779.016 | 0.377 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_site6 | 0.524 | 0.674 | 0.778 | 779.068 | 0.437 |
| fixed | NA | Shannon:hostCeanothus velutinus:inoculum_siteSterile | -2.208 | 1.304 | -1.693 | 782.565 | 0.091 |
| fixed | NA | Shannon:droughtND:inoculum_site2 | 0.018 | 0.642 | 0.028 | 779.055 | 0.978 |
| fixed | NA | Shannon:droughtND:inoculum_site3 | 0.468 | 0.656 | 0.713 | 761.413 | 0.476 |
| fixed | NA | Shannon:droughtND:inoculum_site4 | 0.336 | 0.516 | 0.651 | 780.553 | 0.515 |
| fixed | NA | Shannon:droughtND:inoculum_site5 | -1.160 | 0.814 | -1.425 | 779.215 | 0.155 |
| fixed | NA | Shannon:droughtND:inoculum_site6 | 1.144 | 0.662 | 1.729 | 781.593 | 0.084 |
| fixed | NA | Shannon:droughtND:inoculum_siteSterile | 1.043 | 1.199 | 0.870 | 779.158 | 0.384 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site2 | 3.098 | 2.246 | 1.379 | 783.493 | 0.168 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site3 | 0.031 | 1.488 | 0.021 | 782.971 | 0.984 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site4 | -0.831 | 1.480 | -0.561 | 780.610 | 0.575 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site5 | -2.121 | 1.903 | -1.114 | 781.010 | 0.265 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_site6 | 1.765 | 1.935 | 0.912 | 779.142 | 0.362 |
| fixed | NA | hostCeanothus velutinus:droughtND:inoculum_siteSterile | -2.625 | 2.547 | -1.031 | 780.772 | 0.303 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 | -1.282 | 1.099 | -1.166 | 783.243 | 0.244 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 | -0.417 | 1.000 | -0.417 | 782.862 | 0.677 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 | -0.040 | 0.805 | -0.050 | 781.159 | 0.960 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 | 1.334 | 1.075 | 1.240 | 781.134 | 0.215 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 | -1.164 | 1.046 | -1.113 | 778.965 | 0.266 |
| fixed | NA | Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile | 1.589 | 1.822 | 0.872 | 780.899 | 0.384 |
| ran_pars | block | sd__(Intercept) | 0.339 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.879 | NA | NA | NA | NA |
AMF
Figure 4
Alpha diversity
Effect of Shannon diversity on plant measures
Table 4
## overall_transformed_plant_value ~ Shannon * host * drought *
## inoculum_site + (1 | block)
## <environment: 0x556928702540>
| effect | group | term | estimate | std.error | statistic | df | p.value |
|---|---|---|---|---|---|---|---|
| fixed | NA | (Intercept) | -0.774 | 0.228 | -3.399 | 342 | 0.001 |
| fixed | NA | Shannon | 0.234 | 0.159 | 1.469 | 342 | 0.143 |
| fixed | NA | droughtND | 0.975 | 0.351 | 2.778 | 342 | 0.006 |
| fixed | NA | inoculum_site1 | 0.079 | 0.438 | 0.182 | 342 | 0.856 |
| fixed | NA | inoculum_site2 | 1.292 | 0.612 | 2.111 | 342 | 0.036 |
| fixed | NA | inoculum_site3 | 0.070 | 0.467 | 0.150 | 342 | 0.881 |
| fixed | NA | inoculum_site4 | 0.465 | 0.334 | 1.389 | 342 | 0.166 |
| fixed | NA | inoculum_site5 | 0.680 | 0.588 | 1.157 | 342 | 0.248 |
| fixed | NA | inoculum_site6 | 0.413 | 0.535 | 0.773 | 342 | 0.440 |
| fixed | NA | Shannon:droughtND | -0.151 | 0.222 | -0.677 | 342 | 0.499 |
| fixed | NA | Shannon:inoculum_site1 | -0.150 | 0.271 | -0.552 | 342 | 0.581 |
| fixed | NA | Shannon:inoculum_site2 | -0.579 | 0.297 | -1.945 | 342 | 0.053 |
| fixed | NA | Shannon:inoculum_site3 | -0.152 | 0.259 | -0.586 | 342 | 0.558 |
| fixed | NA | Shannon:inoculum_site4 | -0.238 | 0.227 | -1.045 | 342 | 0.297 |
| fixed | NA | Shannon:inoculum_site5 | -0.321 | 0.328 | -0.976 | 342 | 0.330 |
| fixed | NA | Shannon:inoculum_site6 | -0.258 | 0.295 | -0.876 | 342 | 0.382 |
| fixed | NA | droughtND:inoculum_site1 | 0.288 | 0.651 | 0.443 | 342 | 0.658 |
| fixed | NA | droughtND:inoculum_site2 | -1.133 | 1.025 | -1.105 | 342 | 0.270 |
| fixed | NA | droughtND:inoculum_site3 | -0.941 | 0.592 | -1.588 | 342 | 0.113 |
| fixed | NA | droughtND:inoculum_site4 | -0.362 | 0.581 | -0.623 | 342 | 0.534 |
| fixed | NA | droughtND:inoculum_site5 | 1.175 | 1.236 | 0.951 | 342 | 0.342 |
| fixed | NA | droughtND:inoculum_site6 | -0.880 | 0.740 | -1.190 | 342 | 0.235 |
| fixed | NA | Shannon:droughtND:inoculum_site1 | 0.013 | 0.358 | 0.035 | 342 | 0.972 |
| fixed | NA | Shannon:droughtND:inoculum_site2 | 0.577 | 0.445 | 1.298 | 342 | 0.195 |
| fixed | NA | Shannon:droughtND:inoculum_site3 | 0.346 | 0.335 | 1.030 | 342 | 0.304 |
| fixed | NA | Shannon:droughtND:inoculum_site4 | 0.290 | 0.334 | 0.867 | 342 | 0.386 |
| fixed | NA | Shannon:droughtND:inoculum_site5 | -0.365 | 0.555 | -0.658 | 342 | 0.511 |
| fixed | NA | Shannon:droughtND:inoculum_site6 | 0.506 | 0.389 | 1.302 | 342 | 0.194 |
| ran_pars | block | sd__(Intercept) | 0.000 | NA | NA | NA | NA |
| ran_pars | Residual | sd__Observation | 0.912 | NA | NA | NA | NA |
Comparison between inoculum and root communities
Bacteria
Figure 5
Figure 6
Not all taxa in the inoculae were subsequently found in the root samples
Figure 7
Fungi
Figure 8
Figure 9
Not all taxa in the inoculae were subsequently found in
the root samples
Figure 10
AMF
Figure 11
Figure 12
Not all taxa in the inoculae were subsequently found in the
root samples
Figure 13
Microbial guilds
Bacteria
I couldn’t get a trustworthy annotation of “mutualists” for bacteria, but here are probable pathogens:
Figure 14
Table 5
## value ~ proportion_pathogen * drought + (1 | block)
## <environment: 0x55692d5791c0>
| effect | term | estimate | std.error | statistic | df | p.value | species |
|---|---|---|---|---|---|---|---|
| fixed | (Intercept) | -0.4579 | 0.2353 | -1.9458 | 27.6894 | 0.0619 | Ceanothus |
| fixed | proportion_pathogen | 0.1621 | 0.5053 | 0.3209 | 480.8904 | 0.7484 | Ceanothus |
| fixed | droughtND | 1.5430 | 0.2479 | 6.2243 | 477.2195 | 0.0000 | Ceanothus |
| fixed | proportion_pathogen:droughtND | -2.3112 | 0.6993 | -3.3049 | 477.2112 | 0.0010 | Ceanothus |
| fixed | (Intercept) | -0.3939 | 0.2931 | -1.3441 | 25.3702 | 0.1908 | Abies |
| fixed | proportion_pathogen | 1.0819 | 0.7509 | 1.4409 | 572.5931 | 0.1502 | Abies |
| fixed | droughtND | 0.6770 | 0.3000 | 2.2564 | 575.5163 | 0.0244 | Abies |
| fixed | proportion_pathogen:droughtND | -1.8231 | 0.9838 | -1.8530 | 574.8925 | 0.0644 | Abies |
Fungi
How does the proportion of mutualist fungi relate to indicators of plant health?
In the following figure, the X-axis represents the proportion of fungi that could be identified to a mutualistic guild; the Y-axis represents the value of the various measures of plant success (facets). Y-axis scales vary between facets.
Figure 15
We see an opposite pattern when looking at the proportions of putatively pathogenic fungi
Figure 16
| effect | term | estimate | std.error | statistic | df | p.value | species |
|---|---|---|---|---|---|---|---|
| fixed | (Intercept) | -0.3847 | 0.1554 | -2.4763 | 10.3037 | 0.0321 | Ceanothus |
| fixed | proportion_pathogen | -0.0765 | 0.3571 | -0.2142 | 481.0194 | 0.8305 | Ceanothus |
| fixed | droughtND | 0.6741 | 0.1251 | 5.3868 | 478.1963 | 0.0000 | Ceanothus |
| fixed | proportion_pathogen:droughtND | 0.4320 | 0.4147 | 1.0417 | 479.3039 | 0.2981 | Ceanothus |
| fixed | (Intercept) | -0.0686 | 0.2101 | -0.3265 | 7.1573 | 0.7534 | Abies |
| fixed | proportion_pathogen | -0.1818 | 0.2842 | -0.6398 | 573.1129 | 0.5226 | Abies |
| fixed | droughtND | 0.1919 | 0.0886 | 2.1646 | 573.6108 | 0.0308 | Abies |
| fixed | proportion_pathogen:droughtND | -0.6103 | 0.4252 | -1.4352 | 573.5293 | 0.1518 | Abies |
| fixed | (Intercept) | -0.2647 | 0.1512 | -1.7507 | 10.5999 | 0.1088 | Ceanothus |
| fixed | proportion_mutualist | -0.3757 | 0.2059 | -1.8246 | 478.0381 | 0.0687 | Ceanothus |
| fixed | droughtND | 0.5233 | 0.1298 | 4.0310 | 477.7130 | 0.0001 | Ceanothus |
| fixed | proportion_mutualist:droughtND | 0.7054 | 0.2734 | 2.5804 | 478.2614 | 0.0102 | Ceanothus |
| fixed | (Intercept) | -0.1068 | 0.2240 | -0.4767 | 9.3338 | 0.6446 | Abies |
| fixed | proportion_mutualist | 0.0251 | 0.1663 | 0.1506 | 572.6223 | 0.8803 | Abies |
| fixed | droughtND | 0.1075 | 0.1439 | 0.7472 | 573.1318 | 0.4553 | Abies |
| fixed | proportion_mutualist:droughtND | 0.0540 | 0.2282 | 0.2368 | 574.9668 | 0.8129 | Abies |
Beta-Diversity
Bacteria
Figure 17
Table 7
## PermANOVA run without outlier Sterile-inoculum root samples...
| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| host | 1 | 3.8414120 | 0.0687480 | 12.836684 | 0.001 |
| inoculum_site | 5 | 7.1862718 | 0.1286094 | 4.802812 | 0.001 |
| drought | 1 | 0.8088162 | 0.0144750 | 2.702787 | 0.001 |
| host:inoculum_site | 5 | 3.6135887 | 0.0646707 | 2.415075 | 0.001 |
| host:drought | 1 | 0.7562988 | 0.0135351 | 2.527292 | 0.001 |
| inoculum_site:drought | 5 | 1.9283329 | 0.0345105 | 1.288766 | 0.005 |
| host:inoculum_site:drought | 5 | 1.8316856 | 0.0327808 | 1.224173 | 0.018 |
| Residual | 120 | 35.9103196 | 0.6426704 | NA | NA |
| Total | 143 | 55.8767255 | 1.0000000 | NA | NA |
Fungi
Figure 18
Table 7
## PermANOVA run without outlier Sterile-inoculum root samples...
| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| host | 1 | 1.8555637 | 0.0288094 | 5.687460 | 0.001 |
| inoculum_site | 5 | 14.1030579 | 0.2189636 | 8.645414 | 0.001 |
| drought | 1 | 0.6383236 | 0.0099106 | 1.956516 | 0.007 |
| host:inoculum_site | 5 | 4.4734164 | 0.0694541 | 2.742280 | 0.001 |
| host:drought | 1 | 0.4690934 | 0.0072831 | 1.437811 | 0.082 |
| inoculum_site:drought | 5 | 2.0071801 | 0.0311634 | 1.230436 | 0.052 |
| host:inoculum_site:drought | 5 | 1.7109789 | 0.0265646 | 1.048859 | 0.351 |
| Residual | 120 | 39.1506299 | 0.6078512 | NA | NA |
| Total | 143 | 64.4082440 | 1.0000000 | NA | NA |
AMF
Figure 19
Table 8
## PermANOVA run without outlier Sterile-inoculum root samples...
| term | df | SumOfSqs | R2 | statistic | p.value |
|---|---|---|---|---|---|
| inoculum_site | 6 | 6.9907731 | 0.2129210 | 2.9819777 | 0.001 |
| drought | 1 | 0.3007071 | 0.0091588 | 0.7696159 | 0.777 |
| inoculum_site:drought | 6 | 2.0978089 | 0.0638939 | 0.8948394 | 0.770 |
| Residual | 60 | 23.4434120 | 0.7140263 | NA | NA |
| Total | 73 | 32.8327011 | 1.0000000 | NA | NA |
Important Taxa
These taxa were identified by both Random Forest models and corncob as being important predictors of the various experimental conditions & had significant differential abundance between levels of those variables
Bacteria
Differential Abundance
Figure 20
Relative Abundances of ‘important’ taxa in root samples
Figure 21
Fungi
Differential Abundance
Figure 22
No fungal taxa were found to have significant differential abundance between drought levels
Relative Abundances of ‘important’ taxa in root samples
Figure 23
AMF
Differential Abundance
Figure 24
No fungal taxa were found to have significant differential abundance between drought levels
Relative Abundances of ‘important’ taxa in root samples
Figure 25
Phylogenetic properties
Bacteria
- Still kind of messy
- What specific questions do we need to address with this?
Fungi
- Phylogenetic dispersion is tricky with ITS markers :(
- Could try GhostTree for fungi of interest that come up as ‘unknown’
Network properties
Selected network attributes
Figure 26
Network properties vs Plant Health
(Composite scaled-centered plant health measures)
Table 9
## Plant_Growth_Response ~ species * kingdom * (n_vertices + n_edges +
## mean_dist + mean_betweenness + mean_closeness + global_effic +
## clustering_coeficient + max_degree)
Table 10
| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| (Intercept) | -0.5543907 | 2.1316421 | -0.2600768 | 0.7948531 |
| speciesSnowbrush | 0.6542343 | 2.0842474 | 0.3138947 | 0.7536604 |
| kingdomBacteria | 0.7978266 | 2.1468131 | 0.3716330 | 0.7102375 |
| kingdomFungi | -0.8562899 | 1.6360027 | -0.5234037 | 0.6007986 |
| n_vertices | 0.0291094 | 0.0107670 | 2.7035694 | 0.0069655 |
| n_edges | -0.0024261 | 0.0012869 | -1.8852135 | 0.0596639 |
| mean_dist | 0.1615886 | 0.4334980 | 0.3727550 | 0.7094025 |
| mean_betweenness | -0.0179824 | 0.0069480 | -2.5881320 | 0.0097768 |
| mean_closeness | 3.5648124 | 6.0927745 | 0.5850885 | 0.5586080 |
| global_effic | 0.2433596 | 2.2006359 | 0.1105861 | 0.9119647 |
| clustering_coeficient | -0.0752389 | 0.5987383 | -0.1256624 | 0.9000221 |
| max_degree | -0.0063211 | 0.0050534 | -1.2508744 | 0.2112458 |
| speciesSnowbrush:kingdomBacteria | -2.5890158 | 2.2315970 | -1.1601628 | 0.2462338 |
| speciesSnowbrush:kingdomFungi | NA | NA | NA | NA |
| speciesSnowbrush:n_vertices | -0.0143278 | 0.0070904 | -2.0207346 | 0.0435487 |
| speciesSnowbrush:n_edges | 0.0009879 | 0.0005423 | 1.8215202 | 0.0687988 |
| speciesSnowbrush:mean_dist | -0.1533864 | 0.4203805 | -0.3648752 | 0.7152746 |
| speciesSnowbrush:mean_betweenness | 0.0087602 | 0.0042885 | 2.0427016 | 0.0413195 |
| speciesSnowbrush:mean_closeness | -3.8685083 | 6.0811564 | -0.6361468 | 0.5248128 |
| speciesSnowbrush:global_effic | -0.3158048 | 2.1737739 | -0.1452795 | 0.8845168 |
| speciesSnowbrush:clustering_coeficient | 0.1621361 | 0.5926434 | 0.2735812 | 0.7844578 |
| speciesSnowbrush:max_degree | 0.0049979 | 0.0031582 | 1.5825020 | 0.1138219 |
| kingdomBacteria:n_vertices | -0.0329669 | 0.0121835 | -2.7058628 | 0.0069179 |
| kingdomFungi:n_vertices | -0.0165321 | 0.0091401 | -1.8087389 | 0.0707640 |
| kingdomBacteria:n_edges | 0.0024004 | 0.0030422 | 0.7890472 | 0.4302542 |
| kingdomFungi:n_edges | 0.0016689 | 0.0011998 | 1.3909118 | 0.1645329 |
| kingdomBacteria:mean_dist | -0.1937280 | 0.4375996 | -0.4427060 | 0.6580653 |
| kingdomFungi:mean_dist | 0.1932210 | 0.3090319 | 0.6252461 | 0.5319390 |
| kingdomBacteria:mean_betweenness | 0.0200096 | 0.0073609 | 2.7183639 | 0.0066635 |
| kingdomFungi:mean_betweenness | 0.0098666 | 0.0061194 | 1.6123424 | 0.1071738 |
| kingdomBacteria:mean_closeness | -3.7281546 | 6.0969418 | -0.6114795 | 0.5410083 |
| kingdomFungi:mean_closeness | -1.1787054 | 5.0414341 | -0.2338036 | 0.8151809 |
| kingdomBacteria:global_effic | -0.5827634 | 2.2369624 | -0.2605155 | 0.7945148 |
| kingdomFungi:global_effic | 1.1682005 | 1.7966026 | 0.6502276 | 0.5156808 |
| kingdomBacteria:clustering_coeficient | 0.4787035 | 0.6264813 | 0.7641146 | 0.4449625 |
| kingdomFungi:clustering_coeficient | -0.6050180 | 0.4565936 | -1.3250690 | 0.1854230 |
| kingdomBacteria:max_degree | 0.0182595 | 0.0103733 | 1.7602447 | 0.0786437 |
| kingdomFungi:max_degree | 0.0034425 | 0.0043117 | 0.7984040 | 0.4248081 |
| speciesSnowbrush:kingdomBacteria:n_vertices | 0.0326440 | 0.0120103 | 2.7180067 | 0.0066707 |
| speciesSnowbrush:kingdomFungi:n_vertices | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:n_edges | -0.0025587 | 0.0034005 | -0.7524393 | 0.4519476 |
| speciesSnowbrush:kingdomFungi:n_edges | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:mean_dist | 0.4770298 | 0.4435839 | 1.0753992 | 0.2824314 |
| speciesSnowbrush:kingdomFungi:mean_dist | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:mean_betweenness | -0.0214609 | 0.0063300 | -3.3903559 | 0.0007228 |
| speciesSnowbrush:kingdomFungi:mean_betweenness | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:mean_closeness | 6.3019795 | 6.1167331 | 1.0302852 | 0.3031022 |
| speciesSnowbrush:kingdomFungi:mean_closeness | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:global_effic | 3.5991501 | 2.4129321 | 1.4916085 | 0.1360880 |
| speciesSnowbrush:kingdomFungi:global_effic | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:clustering_coeficient | -1.3580924 | 0.7086829 | -1.9163612 | 0.0555776 |
| speciesSnowbrush:kingdomFungi:clustering_coeficient | NA | NA | NA | NA |
| speciesSnowbrush:kingdomBacteria:max_degree | -0.0102114 | 0.0123216 | -0.8287420 | 0.4074299 |
| speciesSnowbrush:kingdomFungi:max_degree | NA | NA | NA | NA |
_____
Soil chemistry
Overview of soil properties for each inoculum source:
Testing for significant differences between the samples…
Here are the soil properties that differ significantly between inoculum sources. Sterile inoculum soils are set as the intercept. The stats below pretty nicely reflect the obvious patterns in the overall figure.| term | estimate | std.error | statistic | p.value |
|---|---|---|---|---|
| Mn | 1.248 | 0.268 | 4.658 | 0.000 |
| NH4 | 0.770 | 0.268 | 2.875 | 0.004 |
| Fe:inoc_site1 | 1.516 | 0.328 | 4.618 | 0.000 |
| K:inoc_site1 | 0.904 | 0.328 | 2.753 | 0.006 |
| NO3:inoc_site1 | -0.793 | 0.328 | -2.417 | 0.016 |
| TKN:inoc_site1 | 0.735 | 0.328 | 2.240 | 0.026 |
| Zn:inoc_site1 | 1.160 | 0.328 | 3.536 | 0.000 |
| Fe:inoc_site2 | 0.831 | 0.328 | 2.532 | 0.012 |
| K:inoc_site2 | 0.801 | 0.328 | 2.440 | 0.015 |
| Mn:inoc_site2 | -1.081 | 0.328 | -3.294 | 0.001 |
| TKN:inoc_site2 | 0.660 | 0.328 | 2.010 | 0.045 |
| Mn:inoc_site3 | -1.526 | 0.328 | -4.648 | 0.000 |
| NH4:inoc_site3 | -0.976 | 0.328 | -2.973 | 0.003 |
| Zn:inoc_site3 | -0.693 | 0.328 | -2.112 | 0.035 |
| C:N:inoc_site4 | -0.893 | 0.328 | -2.721 | 0.007 |
| EC:inoc_site4 | -1.026 | 0.328 | -3.127 | 0.002 |
| Mn:inoc_site4 | -1.349 | 0.328 | -4.110 | 0.000 |
| B:inoc_site5 | 1.369 | 0.328 | 4.171 | 0.000 |
| Ca:inoc_site5 | 1.192 | 0.328 | 3.631 | 0.000 |
| K:inoc_site5 | 0.683 | 0.328 | 2.080 | 0.038 |
| Mg:inoc_site5 | 0.682 | 0.328 | 2.078 | 0.039 |
| Mn:inoc_site5 | -1.099 | 0.328 | -3.350 | 0.001 |
| NO3:inoc_site5 | 1.854 | 0.328 | 5.649 | 0.000 |
| TKN:inoc_site5 | 1.022 | 0.328 | 3.114 | 0.002 |
| Zn:inoc_site5 | 1.448 | 0.328 | 4.412 | 0.000 |
| B:inoc_site6 | 0.918 | 0.328 | 2.798 | 0.005 |
| Mn:inoc_site6 | -1.535 | 0.328 | -4.678 | 0.000 |
| NH4:inoc_site6 | -0.754 | 0.328 | -2.299 | 0.022 |
| NO3:inoc_site6 | 1.273 | 0.328 | 3.880 | 0.000 |
| Zn:inoc_site6 | 1.290 | 0.328 | 3.932 | 0.000 |